Directing peptide conformation with centrally positioned pre-organized dipeptide segments: studies of a 12-residue helix and beta-hairpin

Secondary structure formation in oligopeptides can be induced by short nucleating segments with a high propensity to form hydrogen bonded turn conformations. Type I/III turns facilitate helical folding while type II'/I' turns favour hairpin formation. This principle is experimentally verified by studies of two designed dodecapeptides, Boc-Val-Phe-Leu-Phe-Val-Aib-Aib-Val-Phe-Leu-Phe-Val-OMe 1 and Boc-Val-Phe-Leu-Phe-Val- (D) Pro- (L) Pro-Val-Phe-Leu-Phe-Val-OMe 2. The N- and C-terminal flanking pentapeptide sequences in both cases are identical. Peptide 1 adopts a largely alpha-helical conformation in crystals, with a small 3(10) helical segment at the N-terminus. The overall helical fold is maintained in methanol solution as evidenced by NMR studies. Peptide 2 adopts an antiparallel beta-hairpin conformation stabilized by 6 interstrand hydrogen bonds. Key nuclear Overhauser effects (NOEs) provide evidence for the antiparallel beta-hairpin structure. Aromatic proton chemical shifts provide a clear distinction between the conformation of peptides 1 (helical) and 2 (beta-hairpin). The proximity of facing aromatic residues positioned at non-hydrogen bonding positions in the hairpin results in extensively ring current shifted proton resonances in peptide 2.

Structural investigation of resorcinol based symmetrical banana mesogens by XRD, NMR and polarization measurements

Synthesis and structural characterization of two novel symmetrical banana mesogens built from resorcinol with seven phenyl rings linked by ester and imine with a terminal dodecyl/dodecyloxy chain has been carried out. Density functional theory (DFT) has been employed for obtaining the geometry optimized structures, the dipole moments and C-13 NMR chemical shifts. The HOPM and DSC studies revealed enantiotropic B-2 and B-7 phases for the dodecyl and dodecyloxy homologs respectively. The powder X-ray studies of both the mesogens indicate the presence of layer ordering. The polarization measurements reveal an anti-ferroelectric switching for the B-2 phase of the dodecyl homolog whose structure has been identified as SmCSPA. The B-7 phase of the dodecyloxy homolog was found to be non-switchable. High resolution C-13 NMR study of the dodecyl homolog in its mesophase has been carried out. C-13-H-1 dipolar couplings obtained from the 2-dimensional separated local field spectroscopy experiment were used to obtain the orientational order parameters of the different segments of the mesogen. Very large C-13-H-1 dipolar couplings observed for the carbons of the central phenyl ring (9.7-12.3 kHz) in comparison to the dipolar couplings of those of the side arm phenyl rings (less than 3 kHz) are a direct consequence of the ordering in the banana phase and the shape of the molecule. From the ratio of the local order parameter values, the bent-angle of the mesogen could be determined in a straight forward manner to be 120.5 degrees.

Organic fluorine involved intramolecular hydrogen bonds in the derivatives of imides: NMR evidence corroborated by DFT based theoretical calculations

The rare occurrence of intramolecular hydrogen bonds (HBs) of the type N-H center dot center dot center dot F-C is detected in the derivatives of imides in a low polarity solvent by using multi-dimensional and multinuclear NMR experiments. The observation of (1h)J(FH), (2h)J(FN), and (2h)J(FF), where the spin magnetization is transmitted through space among the interacting NMR active nuclei, provided strong and unambiguous evidence for the existence of intra-molecular HBs. The variation in the chemical shifts of labile protons depending on physical conditions, such as the solvent dilution and the systematic alteration of temperature confirmed the presence of weak interactions through intramolecular HBs in all the investigated fluorine substituted molecules. The self or cross dimerization of molecules is unequivocally discarded by the analysis of the rates of diffusion obtained using pseudo-two dimensional DOSY experiments. The Density Function Theory (DFT) calculations based on the Quantum Theory of Atoms In Molecules (QTAIM) and Non Covalent Interaction (NCI), are in close agreement with the NMR experimental findings.

A chitotetrose specific lectin from Luffa acutangula :Physico-chemical properties and the assignment of orientation of sugars in the lectin binding site

A chitooligosaccharide specific lectin (Luffa acutangula agglutinin) has been purified from the exudate of ridge gourd fruits by affinity chromatography on soybean agglutininglycopeptides coupled to Sepharose-6B. The affinity purified lectin was found homogeneous by polyacrylamide gel electrophoresis, in sodium dodecyl sulphate-polyacrylamide gels, by gel filtration on Sephadex G-100 and by sedimentation velocity experiments. The relative molecular weight of this lectin is determined to be 48,000 ± 1,000 by gel chromatography and sedimentation equilibrium experiments. The sedimentation coefficient (S20, w) was obtained to be 4·06 S. The Stokes’ radius of the protein was found to be 2·9 nm by gel filtration. In sodium dodecyl sulphate-polyacrylamide gel electrophoresis the lectin gave a molecular weight of 24,000 in the presence as well as absence of 2-mercaptoethanol. The subunits in this dimeric lectin are therefore held by non-covalent interactions alone. The lectin is not a glycoprotein and circular dichroism spectral studies indicate that this lectin has 31% α-helix and no ß-sheet. The lectin is found to bind specifically to chitooligosaccharides and the affinity of the lectin increases with increasing oligosaccharide chain length as monitored by near ultra-violetcircular dichroism and intrinsic fluorescence titration. The values of ΔG, ΔΗ and ΔS for the binding process showed a pronounced dependence on the size of the oligosaccharide. The values for both ΔΗ and ΔS show a significant increase with increase in the oligosaccharide chain length showing that the binding of higher oligomers is progressively more favoured thermodynamically than chitobiose itself. The thermodynamic data is consistent with an extended binding site in the lectin which accommodates a tetrasaccharide. Based on the thermodynamic data, blue shifts and fluorescence enhancement, spatial orientation of chitooligosaccharides in the combining site of the lectin is assigned.

Kinetics and chemical analysis of photoinduced interdiffusion in nanolayered Se/As2S3 films

We have studied the kinetics of photoinduced effects in nanolayered Se/As2S3 film by in situ optical absorption measurements, which reveal that photodarkening in these films is followed by photoinduced diffusion. An increase in disorder during photodarkening and its subsequent decrease during photoinduced diffusion were also observed. The observation of photodarkening of Se at room temperature when confined between As2S3 layers suggests that the glass transition temperature of Se shifts to higher energy. The analysis shows that the atoms which take part in photodarkening play a vital role in photoinduced diffusion. The x-ray photoelectron spectroscopy measurements show the atomic movements during photoinduced diffusion. It also shows that some of the As–S bonds are converted into As–Se bonds. Since it is energetically difficult to break an As–S bond to form an As–Se bond, we assume that the new bond formations are taking place by the bond rearrangement mechanism.

Ab Initio MD Simulations of the Bronsted Acidity of Glutathione in Aqueous Solutions: Predicting pK(a) Shifts of the Cysteine Residue

The tripeptide glutathione (GSH) is one of the most abundant peptides and the major repository for nonprotein sulfur in both animal and plant cells. It plays a critical role in intracellular oxidative stress management by the reversible formation of glutathione disulfide with the thiol-disulfide pair acting as a redox buffer. The state of charge of the ionizable groups of GSH can influence the redox couple, and hence the pK(a) value of the cysteine residue of GSH is critical to its functioning. Here we report ab initio Car-Parrinello molecular dynamics simulations of glutathione solvated by 200 water molecules, all of which are considered in the simulation. We show that the free-energy landscape for the protonation-deprotonation reaction of the cysteine residue of GSH computed using metadynamics sampling provides shift in the dissociation constant values as compared with the isolated accurate estimates of the pK(a) and correctly predicts the cysteine amino acid.

Growth and electron effective mass measurements of strained Si and Si0.94Ge0.06 on relaxed Si0.62Ge0.38 buffers grown by rapid thermal chemical vapor deposition

Abstract: We report the growth and the electron cyclotron resonance measurements of n-type Si/Si0.62Ge0.38 and Si0.94Ge0.06/Si0.62Ge0.38 modulation-doped heterostructures grown by rapid thermal chemical vapor deposition. The strained Si and Si0.94Ge0.06 channels were grown on relaxed Si0.62Ge0.38 buffer layers, which consist of 0.6 mu m uniform Si0.62Ge0.38 layers and 0.5 mu m compositionally graded relaxed SiGe layers from 0 to 38% Ge. The buffer layers were annealed at 800 degrees C for 1 h to obtain complete relaxation. A 75 Angstrom Si(SiGe) channel with a 100 Angstrom spacer and a 300 Angstrom 2 X 10(19) cm(-3) n-type supply layer was grown on the top of the buffer layers. The cross-sectional transmission electron microscope reveals that the dense dislocation network is confined to the buffer layer, and relatively few dislocations terminate on the surface. The plan-view image indicates the threading dislocation density is about 4 X 10(6) cm(-2). The far-infrared measurements of electron cyclotron resonance were performed at 4 K with the magnetic field of 4-8 T. The effective masses determined from the slope of the center frequency of the absorption peak versus applied magnetic field plot are 0.203m(0) and 0.193m(0) for the two dimensional electron gases in the Si and Si0.94Ge0.06 channels, respectively. The Si effective mass is very close to that of a two dimensional electron gas in an Si MOSFET (0.198m(0)). The electron effective mass of Si0.94Ge0.06 is reported for the first time and is about 5% lower than that of pure Si.

Evidence of clustering in an aqueous electrolyte solution: a small-angle X-ray scattering study

The work reported hen was motivated by a desire to verify the existence of structure - specifically MP-rich clusters induced by sodium bromide (NaBr) in the ternary liquid mixture 3-methylpyridine (Mf) + water(W) + NaBr. We present small-angle X-ray scattering (SAXS) measurements in this mixture. These measurements were obtained at room temperature (similar to 298 K) in the one-phase region (below the relevant lower consolute points, T(L)s) at different values of X (i.e., X = 0.02 - 0.17), where X is the weight fraction of NaBr in the mixture. Cluster-size distribution, estimated on the assumption that the clusters are spherical, shows systematic behaviour in that the peak of the distribution shifts rewards larger values of cluster radius as X increases. The largest spatial extent of the clusters (similar to 4.5 nm) is seen at X = 0.17. Data analysis assuming arbitrary shapes and sizes of clusters gives a limiting value of cluster size (- 4.5 nm) that is not very sensitive to X. It is suggested that the cluster size determined may not be the same as the usual critical-point fluctuations far removed from the critical point (T-L). The influence of the additional length scale due to clustering is discussed from the standpoint of crossover from Ising to mean-field critical behaviour, when moving away from the T-L.

Surface chemical studies of Thiobacillus ferrooxidans with reference to copper tolerance

A strain of Thiobacillus ferrooxidans was adapted to grow at higher concentrations of copper by single step culturing in the presence of 20 g/L (0.314 mol/L) cupric ions added to 9K medium. Exposure to copper results in change in the surface chemistry of the microorganism. The isoelectric point of the adapted strain (pI=4.7) was observed to be at a higher pH than that of the wild unadapted strain(pI=2.0). Compared to the wild strain, the copper adapted strain was found to be more hydrophobic and showed enhanced attachment efficiency to the pyrite mineral. The copper adsorption ability of the adapted strain was also found to be higher than that of the wild strain. Fourier transform infrared spectroscopy of adapted cells suggested that a proteinaceous new cell surface component is synthesized by the adapted strain. Treatment of adapted cells with proteinase-K, resulted in complete loss of tolerance to copper, reduction in copper adsorption and hydrophobicity of the adapted cells. These observations strongly suggest a role played by cell surface modifications of Thiobacillus ferrooxidans in imparting the copper tolerance to the cells and bioleaching of sulphide minerals.

Surface chemical studies on mica and galena using dextrin

The interactions of dextrin with biotite mica and galena have been investigated through adsorption, flotation, and electrokinetic measurements. The adsorption densities of dextrin onto mica continuously increase with increase of pH, while those onto galena show a maximum at pH 11.5. It is observed that the adsorption density of dextrin onto galena is quite high compared to that on mica. Both the adsorption isotherms exhibit Langmuirian behavior. Electrokinetic measurements portray conformational rearrangements of macromolecules with the loading, resulting in a shift of the shear plane, further away from the interface. Dissolution experiments indicate release of the lattice metal ions from mica and galena. Coprecipitation tests confirm polymer-metal ion interaction in the bulk solution. Dextrin does not exhibit any depressant action toward mica, whereas, with galena, the flotation recovery is decreased with an increase in pH beyond 9, in the presence of dextrin, complementing the adsorption results. Differential flotation results on a synthetic mixture of mica and galena show that mica can be selectively separated from galena using dextrin as a depressant for galena above pH 10. Possible mechanisms of interaction between dextrin and mica/galena are discussed.

The role of lysine-41 in RNase A catalysis - A quantum chemical study on the active site ligand complex

Several mechanisms have been proposed to explain the action of enzymes at the atomic level. Among them, the recent proposals involving short hydrogen bonds as a step in catalysis by Gerlt and Gassman [1] and proton transfer through low barrier hydrogen bonds (LBHBs) [2, 3] have attracted attention. There are several limitations to experimentally testing such hypotheses, Recent developments in computational methods facilitate the study of active site-ligand complexes to high levels of accuracy, Our previous studies, which involved the docking of the dinucleotide substrate UpA to the active site of RNase A [4, 5], enabled us to obtain a realistic model of the ligand-bound active site of RNase A. From these studies, based on empirical potential functions, we were able to obtain the molecular dynamics averaged coordinates of RNase A, bound to the ligand UpA. A quantum mechanical study is required to investigate the catalytic process which involves the cleavage and formation of covalent bonds. In the present study, we have investigated the strengths of some of the hydrogen bonds between the active site residues of RNase A and UpA at the ab initio quantum chemical level using the molecular dynamics averaged coordinates as the starting point. The 49 atom system and other model systems were optimized at the 3-21G level and the energies of the optimized systems were obtained at the 6-31G* level. The results clearly indicate the strengthening of hydrogen bonds between neutral residues due to the presence of charged species at appropriate positions. Such a strengthening manifests itself in the form of short hydrogen bonds and a low barrier for proton transfer. In the present study, the proton transfer between the 2'-OH of ribose (from the substrate) and the imidazole group from the H12 of RNase A is influenced by K41, which plays a crucial role in strengthening the neutral hydrogen bond, reducing the barrier for proton transfer.

Field imperfection induced axial secular frequency shifts in nonlinear ion traps

This article develops a simple analytical expression that relates ion axial secular frequency to field aberration in ion trap mass spectrometers. Hexapole and octopole aberrations have been considered in the present computations. The equation of motion of the ions in a pseudopotential well with these superpositions has the form of a Duffing-like equation and a perturbation method has been used to obtain the expression for ion secular frequency as a function of field imperfections. The expression indicates that the frequency shift is sensitive to the sign of the octopole superposition and insensitive to the sign of the hexapole superposition. Further, for weak multipole superposition of the same magnitude, octopole superposition causes a larger frequency shift in comparison to hexapole superposition.

Homogeneous precipitation from solution by urea hydrolysis: a novel chemical route to the a-hydroxides of nickel and cobalt

Homogeneous precipitation from solution by hydrolysis of urea at elevated temperatures (T=120 degrees C) yields novel ammonia-intercalated alpha-type hydroxide phases of the formula M(OH)(x)(NH3)(0.4)(H2O)(y)(NO3)(2-x) where x=2, y=0.68 for M=Ni and x=1.85, y=0 for M=Co. These triple-layered hexagonal phases (a=3.08+/-0.01 Angstrom, c=21.7+/-0.05 Angstrom) are more crystalline than similar phases obtained by chemical precipitation or electrosynthesis. This method can be adapted as a convenient chemical route to the bulk synthesis of alpha-hydroxides.

Chemical Modification Studies of Gelonin - Involvement of Arginine Residues in Biological-Activity

Gelonin inhibits protein synthesis by inactivating the eukaryotic 60 S ribosomal subunit by an unknown mechanism. The protein was purified in high yield by a new method using Cibacron blue F3GA-Sepharose. Chemical modification studies reveal that arginine residues are essential for biological activity.

Assignment of fundamental vibrations of. ,N'-dimethylthiourea,

The infrared spectra of symmetric N,N′-dimethylthiourea (s-DMTU) and its N-deuterated (s-DMTU-d2) species have been measured. The fundamental frequencies have been assigned by comparison with the assignments in structurally related molecules and the infrared band shifts on N-deuteration, S-methylation, available Raman data and with the aid of theoretical band assignments from normal coordinate treatments for s-DMTU-d0 and -d2. A force field is derived for s-DMTU by transferring the force constants chiefly from N-methylthiourea and the subsequent refinement of the force constants by a least squares procedure.